Tidyr function gather and paste inside loop
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I'm trying to run a loop with multiple dataframes. I'm using the gather function from tidyr and I want to use as argument the index of the loop, i, along with a word, deaths.
I've been trying:
gather(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
However, everytime I try that, it returns "Error: Must supply a symbol or a string as argument".
I read somewhere that tidyr evaluates things in a non-standard way and that the alternative is gather_, which uses standard evaluation.
However, the command
gather_(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
Returns Error: Only strings can be converted to symbols.
However, I tought the paste command was already resulting in a string.
Anyone knows a fix?
Here is the full error:
"<error>
message: Only strings can be converted to symbols
class: `rlang_error`
backtrace:
-tidyr::gather_(...)
-tidyr:::gather_.data.frame(...)
-rlang::syms(gather_cols)
-rlang:::map(x, sym)
-base::lapply(.x, .f, ...)
-rlang:::FUN(X[[i]], ...)
Call `summary(rlang::last_error())` to see the full backtrace"
The full code:
require(datasus)
require(tidyr)
data_list <- list()
for(i in 1:2){
data_list[[i]] <- sim_inf10_mun(linha = "Município", coluna = "Ano do Óbito", periodo = c(1996:2016), municipio = "all",
capitulo_cid10 = i)
data_list[[i]] <- data.frame(data_list[i])
data_list[[i]] <- data_list[[i]][-1,]
data_list[[i]] <- data_list[[i]][,-ncol(data_list[[i]])]
data_list[[i]] <- gather(data_list[[i]], "ano", "deaths_01_i", 2:ncol(data_list[[i]]))
names(data_list[[i]])[1]<-"cod_mun"
data_list[[i]] <- transform(data_list[[i]], cod_mun = substr(cod_mun, 1, 6))
data_list[[i]] <- transform(data_list[[i]], ano = substr(ano, 2, 5))
}
This returns a panel dataset exactly the way I want, with (municipality code-year) identification in lines, and a value. My problem is that the value (column) name is "deaths_01_i", which is kinda obvious since it is quotation marks, whereas I wanted it to run with the loop. Thus I tried to implement it with a paste.
I know I can just change the variable name by adding a line names(data_list[[i]])[3]<-paste("deaths_01",i,sep="_"), but the problem got my attention to improving my understanding of the code.
Some words are in Portuguese but they are irrelevant to the problem. I also changed the range of the loop to avoid time issues.
r tidyr
asked Nov 9 at 16:02
jpugliese
185
|
show 2 more comments
up vote
1
down vote
favorite
I'm trying to run a loop with multiple dataframes. I'm using the gather function from tidyr and I want to use as argument the index of the loop, i, along with a word, deaths.
I've been trying:
gather(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
However, everytime I try that, it returns "Error: Must supply a symbol or a string as argument".
I read somewhere that tidyr evaluates things in a non-standard way and that the alternative is gather_, which uses standard evaluation.
However, the command
gather_(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
Returns Error: Only strings can be converted to symbols.
However, I tought the paste command was already resulting in a string.
Anyone knows a fix?
Here is the full error:
"<error>
message: Only strings can be converted to symbols
class: `rlang_error`
backtrace:
-tidyr::gather_(...)
-tidyr:::gather_.data.frame(...)
-rlang::syms(gather_cols)
-rlang:::map(x, sym)
-base::lapply(.x, .f, ...)
-rlang:::FUN(X[[i]], ...)
Call `summary(rlang::last_error())` to see the full backtrace"
The full code:
require(datasus)
require(tidyr)
data_list <- list()
for(i in 1:2){
data_list[[i]] <- sim_inf10_mun(linha = "Município", coluna = "Ano do Óbito", periodo = c(1996:2016), municipio = "all",
capitulo_cid10 = i)
data_list[[i]] <- data.frame(data_list[i])
data_list[[i]] <- data_list[[i]][-1,]
data_list[[i]] <- data_list[[i]][,-ncol(data_list[[i]])]
data_list[[i]] <- gather(data_list[[i]], "ano", "deaths_01_i", 2:ncol(data_list[[i]]))
names(data_list[[i]])[1]<-"cod_mun"
data_list[[i]] <- transform(data_list[[i]], cod_mun = substr(cod_mun, 1, 6))
data_list[[i]] <- transform(data_list[[i]], ano = substr(ano, 2, 5))
}
This returns a panel dataset exactly the way I want, with (municipality code-year) identification in lines, and a value. My problem is that the value (column) name is "deaths_01_i", which is kinda obvious since it is quotation marks, whereas I wanted it to run with the loop. Thus I tried to implement it with a paste.
I know I can just change the variable name by adding a line names(data_list[[i]])[3]<-paste("deaths_01",i,sep="_"), but the problem got my attention to improving my understanding of the code.
Some words are in Portuguese but they are irrelevant to the problem. I also changed the range of the loop to avoid time issues.
r tidyr
asked Nov 9 at 16:02
jpugliese
185
2
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
2
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
try add double "!" before your paste(), such likegather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
– Darren Tsai
Nov 9 at 17:03
|
show 2 more comments
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I'm trying to run a loop with multiple dataframes. I'm using the gather function from tidyr and I want to use as argument the index of the loop, i, along with a word, deaths.
I've been trying:
gather(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
However, everytime I try that, it returns "Error: Must supply a symbol or a string as argument".
I read somewhere that tidyr evaluates things in a non-standard way and that the alternative is gather_, which uses standard evaluation.
However, the command
gather_(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
Returns Error: Only strings can be converted to symbols.
However, I tought the paste command was already resulting in a string.
Anyone knows a fix?
Here is the full error:
"<error>
message: Only strings can be converted to symbols
class: `rlang_error`
backtrace:
-tidyr::gather_(...)
-tidyr:::gather_.data.frame(...)
-rlang::syms(gather_cols)
-rlang:::map(x, sym)
-base::lapply(.x, .f, ...)
-rlang:::FUN(X[[i]], ...)
Call `summary(rlang::last_error())` to see the full backtrace"
The full code:
require(datasus)
require(tidyr)
data_list <- list()
for(i in 1:2){
data_list[[i]] <- sim_inf10_mun(linha = "Município", coluna = "Ano do Óbito", periodo = c(1996:2016), municipio = "all",
capitulo_cid10 = i)
data_list[[i]] <- data.frame(data_list[i])
data_list[[i]] <- data_list[[i]][-1,]
data_list[[i]] <- data_list[[i]][,-ncol(data_list[[i]])]
data_list[[i]] <- gather(data_list[[i]], "ano", "deaths_01_i", 2:ncol(data_list[[i]]))
names(data_list[[i]])[1]<-"cod_mun"
data_list[[i]] <- transform(data_list[[i]], cod_mun = substr(cod_mun, 1, 6))
data_list[[i]] <- transform(data_list[[i]], ano = substr(ano, 2, 5))
}
This returns a panel dataset exactly the way I want, with (municipality code-year) identification in lines, and a value. My problem is that the value (column) name is "deaths_01_i", which is kinda obvious since it is quotation marks, whereas I wanted it to run with the loop. Thus I tried to implement it with a paste.
I know I can just change the variable name by adding a line names(data_list[[i]])[3]<-paste("deaths_01",i,sep="_"), but the problem got my attention to improving my understanding of the code.
Some words are in Portuguese but they are irrelevant to the problem. I also changed the range of the loop to avoid time issues.
r tidyr
asked Nov 9 at 16:02
jpugliese
185
I'm trying to run a loop with multiple dataframes. I'm using the gather function from tidyr and I want to use as argument the index of the loop, i, along with a word, deaths.
I've been trying:
gather(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
However, everytime I try that, it returns "Error: Must supply a symbol or a string as argument".
I read somewhere that tidyr evaluates things in a non-standard way and that the alternative is gather_, which uses standard evaluation.
However, the command
gather_(data[[i]], "year", paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
Returns Error: Only strings can be converted to symbols.
However, I tought the paste command was already resulting in a string.
Anyone knows a fix?
Here is the full error:
"<error>
message: Only strings can be converted to symbols
class: `rlang_error`
backtrace:
-tidyr::gather_(...)
-tidyr:::gather_.data.frame(...)
-rlang::syms(gather_cols)
-rlang:::map(x, sym)
-base::lapply(.x, .f, ...)
-rlang:::FUN(X[[i]], ...)
Call `summary(rlang::last_error())` to see the full backtrace"
The full code:
require(datasus)
require(tidyr)
data_list <- list()
for(i in 1:2){
data_list[[i]] <- sim_inf10_mun(linha = "Município", coluna = "Ano do Óbito", periodo = c(1996:2016), municipio = "all",
capitulo_cid10 = i)
data_list[[i]] <- data.frame(data_list[i])
data_list[[i]] <- data_list[[i]][-1,]
data_list[[i]] <- data_list[[i]][,-ncol(data_list[[i]])]
data_list[[i]] <- gather(data_list[[i]], "ano", "deaths_01_i", 2:ncol(data_list[[i]]))
names(data_list[[i]])[1]<-"cod_mun"
data_list[[i]] <- transform(data_list[[i]], cod_mun = substr(cod_mun, 1, 6))
data_list[[i]] <- transform(data_list[[i]], ano = substr(ano, 2, 5))
}
This returns a panel dataset exactly the way I want, with (municipality code-year) identification in lines, and a value. My problem is that the value (column) name is "deaths_01_i", which is kinda obvious since it is quotation marks, whereas I wanted it to run with the loop. Thus I tried to implement it with a paste.
I know I can just change the variable name by adding a line names(data_list[[i]])[3]<-paste("deaths_01",i,sep="_"), but the problem got my attention to improving my understanding of the code.
Some words are in Portuguese but they are irrelevant to the problem. I also changed the range of the loop to avoid time issues.
r tidyr
r tidyr
asked Nov 9 at 16:02
jpugliese
185
asked Nov 9 at 16:02
jpugliese
185
edited Nov 9 at 16:57
asked Nov 9 at 16:02
jpugliese
185
asked Nov 9 at 16:02
jpugliese
185
asked Nov 9 at 16:02
jpugliese
185
185
2
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
2
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
try add double "!" before your paste(), such likegather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
– Darren Tsai
Nov 9 at 17:03
|
show 2 more comments
2
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
2
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
try add double "!" before your paste(), such likegather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))
– Darren Tsai
Nov 9 at 17:03
2
2
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
2
2
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
try add double "!" before your paste(), such like
gather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))– Darren Tsai
Nov 9 at 17:03
try add double "!" before your paste(), such like
gather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))– Darren Tsai
Nov 9 at 17:03
|
show 2 more comments
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2
Providing same sample data and desired output would increase the chances for an actual solution.
– Wimpel
Nov 9 at 16:17
2
Please provide sample code, the problem is elsewhere: functional programming + tidyverse + for loop = you are doing something very wrong.
– JohnCoene
Nov 9 at 16:19
@JohnCoene thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
@Wimpel thanks for the reply, I've provided the sample code. The data is downloaded directly using the code.
– jpugliese
Nov 9 at 16:28
try add double "!" before your paste(), such like
gather(data[[i]], "year", !!paste("deaths", i, sep="_"), 2:ncol(data[[i]]))– Darren Tsai
Nov 9 at 17:03